https://github.com/sysbiochalmers/reproduce
Assesing the quality and reproducibility of absolute proteomic data
https://github.com/sysbiochalmers/reproduce
proteomics reproducible-research
Last synced: 3 months ago
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Assesing the quality and reproducibility of absolute proteomic data
- Host: GitHub
- URL: https://github.com/sysbiochalmers/reproduce
- Owner: SysBioChalmers
- License: mit
- Created: 2018-07-12T12:08:38.000Z (almost 8 years ago)
- Default Branch: master
- Last Pushed: 2021-02-26T17:41:34.000Z (over 5 years ago)
- Last Synced: 2025-01-30T22:51:20.661Z (over 1 year ago)
- Topics: proteomics, reproducible-research
- Language: PostScript
- Size: 43.8 MB
- Stars: 1
- Watchers: 3
- Forks: 2
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
- License: LICENSE.md
Awesome Lists containing this project
README
reproduce
=========
[](https://zenodo.org/badge/latestdoi/140708206)
Assessing the quality and reproducibility of absolute proteomic data. Companion repository to the publication [_"Benchmarking accuracy and precision of intensity‐based absolute quantification of protein abundances in Saccharomyces cerevisiae"_](https://doi.org/10.1002/pmic.202000093).
This repository is administered by Benjamín J. Sánchez ([@BenjaSanchez](https://github.com/benjasanchez)), Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology.
Requirements
------------
* [R](https://www.r-project.org/) (tested with v3.6)
* [RStudio](https://rstudio.com/) (tested with v1.2)
* [Rtools](https://cran.r-project.org/bin/windows/Rtools/) (in case of a windows setup)
* [Git](https://git-scm.com/) (or any Git client of your choice, e.g. [Github Desktop](https://desktop.github.com/))
Installation
------------
* Clone locally this repository.
* From the command window in RStudio, run each line in `requirements.txt`.
Usage
-----
All analysis can be reproduced by knitting the RMarkdown file `code/iBAQstudy.Rmd`
Repository Structure
--------------------
|- code/ # all programmatic code relating to the project
| +- templates/ # scripts for generating template files
|
|- data/ # all data from the study
| |- raw_internal/ # raw data generated in-lab or by collaborators, will not be altered
| |- raw_external/ # data from third-party sources, databases etc, will not be altered
| +- colormaps/ # color palettes used for all figures
|
|- doc/ # documentation for the study and other explanatory material
| +- paper/ # contains the generated pdf from knitting the markdown file
|
|- results # all output from workflows and analyses
| |- figures/ # graphs, designated for manuscript figures
| +- pictures/ # diagrams, images, and other non-graph graphics
|
|- .gitignore # files that will not sync to Github
|- LICENSE # license
|- README.md # the top level description of content
|- reproduce.Rproj # contains project information used to customize the behavior of RStudio
+- requirements.txt # the requirements file for reproducing the analysis environment
Acknowledgements
----------------
The initial file and directory structure of this project was developed by a group of participants in the Reproducible Science Curriculum Workshop, held at [NESCent] in December 2014. The structure is based on, and heavily follows the one proposed by [Noble 2009], with a few but small modifications. The [original repository] has been modified to the [reproducible-research-init repository] and adapted to this project.
[original repository]: https://github.com/Reproducible-Science-Curriculum/rr-init
[reproducible-research-init repository]: https://github.com/EngqvistLab/reproducible-research-init
[NESCent]: http://nescent.org
[Noble 2009]: http://dx.doi.org/10.1371/journal.pcbi.1000424